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Gut microbial interactions based on network construction and bacterial pairwise cultivation

Science China Life Sciences 2024年第8期 1751-1762页

作者： Min-Zhi Jiang Chang Liu Chang Xu He Jiang Yulin Wang Shuang-Jiang Liu state key laboratory of microbial Technology Shandong University state key laboratory of microbial resources and Environmental Microbiology Research Center (EMRC)Institute of MicrobiologyChinese Academy of Sciences University of Chinese Academy of Sciences

Association networks are widely applied for the prediction of bacterial interactions in studies of human gut microbiomes.However,the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated bacteria.In this study,we addressed this challenge by integrating in vitro time series network(TSN) associations and cocultivation of TSN taxon pairs.Fecal samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 days.Enriched cells were harvested for DNA extraction and metagenomic sequencing.A total of 198 metagenome-assembled genomes(MAGs) were recovered.Temporal dynamics of bacteria growing on the YCFA agar were used to infer microbial association networks.To experimentally validate the interactions of taxon pairs in networks,we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank,respectively,for pairwise co-cultures.The co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism(51.67%),followed by commensalism(21.67%),amensalism(18.33%),competition(5%) and exploitation(3.33%).Genome-centric analysis further revealed that the commensal gut bacteria(helpers and beneficiaries) might interact with each other via the exchanges of amino acids with high biosynthetic costs,short-chain fatty acids,and/or vitamins.We also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7% of these strains was significantly promoted.This approach provides new insights into the gut microbiome complexity and microbial interactions in association networks.Our work highlights that the positive relationships in gut microbial communities tend to be overestimated,and that amino acids,short-chain fatty acids,and vitamins are contributed to the positive relationships.

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The human-derived novel gut commensal Luoshenia tenuis regulates body weight and food intake in mice

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Food Science and Human Wellness 2024年第2期13卷 830-841页

作者： Yu Jiang Mengxuan Du Lisheng Xie Minzhi Jiang Yaokun Zhang Mingxia Bi Chang Liu Hongwei Liu Shuangjiang Liu state key laboratory of microbial Technology Shandong UniversityQingdao 266237China state key laboratory of microbial resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China College of Life Science Hebei UniversityBaoding 071000China state key laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China

Many studies have revealed that gut microbes modulate host metabolism.In this study,we characterized the therapeutic effects of a novel gut commensal Luoshenia tenuis against host metabolic disorders.First,by in silico analysis,we demonstrated that the L.tenuis was prevalent in the gut microbiomes of healthy humans but were depleted specifically in obesity cohorts.Further in vitro cultivation revealed that L.tenuis produced short chain fatty acids that were verified to modulate host metabolism and some other volatile metabolites to benefit hosts by anti-inflammation and anti-tumor.Second,gavage of the L.tenuis significantly decreased the body weight gain and food intake of high-fat diet-feeding C57BL/6J mice,which was in parallel with the changed expression level of genes related to satiety and feeding behavior.We then performed the gavage trial using diet induced obese mice,and it revealed that the administration of L.tenuis alleviated significantly the abnormal glucose and lipid metabolisms and reduced the inflammatory response.In summary,this study revealed a previously-unknown human gut commensal microbe that benefited host metabolism,and set the stage for the development of novel next-generation probiotic applicable for treatment of obesity and related metabolic disorders.

关键词： Luoshenia tenuis Gut microbe Feeding behavior Obesity Next-generation probiotic

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Beyond microbial carbon use efficiency

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National Science Review 2024年第4期11卷 33-35页

作者： Ke-Qing Xiao Chao Liang Zimeng Wang Jingjing Peng Yao Zhao Ming Zhang Mingyu Zhao Shuiqing Chen Yong-Guan Zhu Caroline L.Peacock state key Lab of Urban and Regional Ecology Research Center for Eco-Environmental SciencesChinese Academy of Sciences University of Chinese Academy of Sciences institute of Applied Ecology Chinese Academy of Sciences Department of environmental Science and Engineering Fudan University College of resources and environmental Sciences China Agricultural University state key laboratory of environmental Criteria and Risk Assessment Chinese Research Academy of Environmental Sciences state key laboratory of Agricultural microbiology College of Resources and Environment Huazhong Agricultural University key laboratory of Cenozoic Geology and Environment Institute of Geology and Geophysics Chinese Academy of Sciences School of Earth and Environment University of Leeds

microbial carbon use efficiency (CUE)is defined as the proportion of microbial biomass growth C versus substrate C uptake, and thus provides a useful measure of microbially driven accumulation and loss of soil organic carbon (SOC)[1]. In a recent study published in Nature [2],the authors used a data-driven machinelearning approach to conclude that CUE promotes global SOC storage based on a positive correlation between CUE and SOC content and that, based on sensitivity analysis, CUE is at least four times as important as six other evaluated factors,namely plant C inputs, C input allocation, non-microbial C transfer, substrate decomposability, environmental modifications and vertical transport.

关键词： SOIL-CARBON ORGANIC-MATTER

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Integrated application of synthetic community reduces consumption of herbicide in field Phalaris minor control

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Soil Ecology Letters 2024年第2期6卷 125-136页

作者： Amina Hadayat Zahir Ahmad Zahir Peng Cai Chun-Hui Gao National key laboratory of Agricultural microbiology College of Resources and EnvironmentHuazhong Agricultural UniversityWuhan430070China Soil microbiology and Biochemistry laboratory Institute of Soil and Environmental SciencesUniversity of AgricultureFaisalabadPakistan

Herbicide-based weeds control impacts wheat crops as well.SynComs of Pseudomonas strains reduce the need for high-dose herbicides.100%Axial provides less weed control compared to 75%Axial with C4 SynCom.Axial 75%with ... 详细信息

关键词： weed control synthetic microbial communities Phalaris minor wheat growth promotion synergistic effect

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Population genomic data reveal low genetic diversity,divergence and local adaptation among threatened Reeves's Pheasant(Syrmaticus reevesii)

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Avian research 2024年第1期15卷 1-11页

作者： Qi Lu Pengcheng Wang Jiang Chang De Chen Shenghan Gao Jacob Hoglund Zhengwang Zhang Ministry of Education key laboratory for Biodiversity Science and Ecological Engineering College of Life SciencesBeijing Normal UniversityBeijing100875China Jiangsu key laboratory for Biodiversity and Biotechnology College of Life SciencesNanjing Normal UniversityNanjing210023China state key laboratory of environmental Criteria and Risk Assessment Chinese Research Academy of Environmental SciencesBeijing100012China state key laboratory of microbial resources Institute of MicrobiologyChinese Academy of SciencesBeijing100101China Department of Ecology and Genetics Animal EcologyUppsala UniversityUppsalaSweden

Population genomic data could provide valuable information for conservation efforts;however,limited studies have been conducted to investigate the genetic status of threatened pheasants.Reeves’s Pheasant(Syrmaticus reevesii)is facing population decline,attributed to increases in habitat loss.There is a knowledge gap in understanding the genomic status and genetic basis underlying the local adaptation of this threatened bird.Here,we used population genomic data to assess population structure,genetic diversity,inbreeding patterns,and genetic divergence.Furthermore,we identified candidate genes linked with adaptation across the current distribution of Reeves’s Pheasant.The present study assembled the first de novo genome sequence of Reeves’s Pheasant and annotated 19,458 genes.We also sequenced 30 individuals from three populations(Dabie Mountain,Shennongjia,Qinling Mountain)and found that there was clear population structure among those populations.By comparing with other threatened species,we found that Reeves’s Pheasants have low genetic diversity.Runs of homozygosity suggest that the Shennongjia population has experienced serious inbreeding.The demographic history results indicated that three populations experienced several declines during the glacial period.Local adaptative analysis among the populations identified 241 candidate genes under directional selection.They are involved in a large variety of processes,including the immune response and pigmentation.Our results suggest that the three populations should be considered as three different conservation units.The current study provides genetic evidence for conserving the threatened Reeves’s Pheasant and provides genomic resources for global biodiversity management.

关键词： Conservation genetics Local adaptation Pheasant Whole-genome sequencing

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Afforestation with an age-sequence of Mongolian pine plantation promotes soil microbial residue accumulation in the Horqin Sandy Land, China

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Journal of Arid Land 2024年第4期16卷 567-579页

作者： GUO Jingwen SONG Xueshu WANG Xiao DU Zhangliu LU Sen state key laboratory of Efficient Production of Forest resources Research Institute of ForestryChinese Academy of ForestryBeijing 100091China Co-Innovation center for Sustainable Forestry in Southern China Nanjing Forestry UniversityNanjing 210037China College of resources and environmental Sciences China Agricultural UniversityBeijing 100193China

Land use change affects the balance of organic carbon(C)reserves and the global C cycle.microbial residues are essential constituents of stable soil organic C(SOC).However,it remains unclear how microbial residue changes over time following afforestation.In this study,16-,23-,52-,and 62-year-old Mongolian pine stands and 16-year-old cropland were studied in the Horqin Sandy Land,China.We analyzed changes in SOC,amino sugar content,and microbial parameters to assess how microbial communities influence soil C transformation and preservation.The results showed that SOC storage increased with stand age in the early stage of afforestation but remained unchanged at about 1.27-1.29 kg/m2 after 52 a.Moreover,there were consistent increases in amino sugars and microbial residues with increasing stand age.As stand age increased from 16 to 62 a,soil pH decreased from 6.84 to 5.71,and the concentration of total amino sugars increased from 178.53 to 509.99 mg/kg.A significant negative correlation between soil pH and the concentration of specific and total amino sugars was observed,indicating that the effects of soil acidification promote amino sugar stabilization during afforestation.In contrast to the Mongolian pine plantation of the same age,the cropland accumulated more SOC and microbial residues because of fertilizer application.Across Mongolian pine plantation with different ages,there was no significant change in calculated contribution of bacterial or fungal residues to SOC,suggesting that fungi were consistently the dominant contributors to SOC with increasing time.Our results indicate that afforestation in the Horqin Sandy Land promotes efficient microbial growth and residue accumulation in SOC stocks and has a consistent positive impact on SOC persistence.

关键词： soil organic matter stand age biomarker amino sugars microbial residues

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Different mechanisms underlie similar species-area relationships in two tropical archipelagoes

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Plant Diversity 2024年第2期46卷 238-246页

作者： Shengchun Li Tieyao Tu Shaopeng Li Xian Yang Yong Zheng Liang-Dong Guo Dianxiang Zhang Lin Jiang key laboratory of Plant resources Conservation and Sustainable Utilization South China Botanical GardenChinese Academy of SciencesGuangzhou 510650China ECNU-Alberta Joint Lab for Biodiversity Study Tiantong Forest Ecosystem National Observation and Research StationSchool of Ecological and Environmental SciencesEast China Normal UniversityShanghai 200241China School of Biological Sciences Georgia Institute of TechnologyAtlantaGA 30332USA Jiangxi Academy of Forestry Nanchang 330032China institute of Eco-Chongming(IEC) Shanghai 202162China state key laboratory of Biocontrol School of EcologySun Yat-sen UniversityGuangzhou 510275China School of Geographical Sciences Fujian Normal UniversityFuzhou 350007China state key laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China

Despite much research in the field of island biogeography,mechanisms regulating insular diversity remain elusive.Here,we aim to explore mechanisms underlying plant species-area relationships in two tropical archipelagoes in the South China Sea.We found positive plant species-area relationships for both coral and continental archipelagoes.However,our results showed that different mechanisms contributed to similar plant species-area relationships between the two archipelagoes.For coral islands,soil nutrients and spatial distance among communities played major roles in shaping plant community structure and species diversity.By contrast,the direct effect of island area,and to a lesser extent,soil nutrients determined plant species richness on continental islands.Intriguingly,increasing soil nutrients availability(N,P,K)had opposite effects on plant diversity between the two archipelagoes.In summary,the habitat quality effect and dispersal limitation are important for regulating plant diversity on coral islands,whereas the passive sampling effect,and to a lesser extent,the habitat quality effect are important for regulating plant diversity on continental islands.More generally,our findings indicate that island plant species-area relationships are outcomes of the interplay of both niche and neutral processes,but the driving mechanisms behind these relationships depends on the type of islands.

关键词： Coral and continental islands Plant diversity Soil nutrients Species-area relationships The sampling effect

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Ecology and risks of the global plastisphere as a newly expanding microbial habitat

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The Innovation 2024年第1期5卷 49-58页

作者： Changchao Li Michael RGillings Chao Zhang Qinglin Chen Dong Zhu Jie Wang Kankan Zhao Qicheng Xu Polly Hangmei Leung Xiangdong Li Jian Liu Ling Jin Department of Civil and environmental Engineering The Hong Kong Polytechnic UniversityKowloonHong KongChina Environment research institute Shandong UniversityQingdao 266237China state key laboratory of Marine Pollution City University of Hong KongKowloon TongHong KongChina ARC Centre of Excellence in Synthetic Biology Faculty of Science and EngineeringMacquarie UniversitySydneyNSW 2109Australia key laboratory of Urban Environment and Health Ningbo Urban Environment Observation and Research StationInstitute of Urban EnvironmentChinese Academy of SciencesXiamen 361021China Beijing key laboratory of Farmland Soil Pollution Prevention and Remediation College of Resources and Environmental SciencesChina Agricultural UniversityBeijing 100193China institute of Soil and Water resources and environmental Science College of Environmental and Resource SciencesZhejiang UniversityHangzhou 310058China Jiangsu Collaborative Innovation center for Solid Organic Waste Resource Utilization Nanjing Agricultural UniversityNanjing 210095China Department of Health Technology and Informatics and research institute for Future Food The Hong Kong Polytechnic UniversityKowloonHong KongChina Southern Marine Science and Engineering Guangdong laboratory(Guangzhou) Guangzhou 511458China

Plastic offers a new niche for microorganisms,the plastisphere.The everincreasing emission of plastic waste makes it critical to understand the microbial ecology of the plastisphere and associated effects.Here,we present a global fingerprint of the plastisphere,analyzing samples collected from freshwater,seawater,and terrestrial ecosystems.The plastisphere assembles a distinct microbial community that has a clearly higher heterogeneity and a more deterministically dominated assembly compared to natural habitats.New coexistence patterns—loose and fragile networks with mostly specialist linkages among microorganisms that are rarely found in natural habitats—are seen in the plastisphere.Plastisphere microbiomes generally have a great potential to metabolize organic compounds,which could accelerate carbon turnover.Microorganisms involved in the nitrogen cycle are also altered in the plastisphere,especially in freshwater plastispheres,where a high abundance of denitrifiers may increase the release of nitrite(aquatic toxicant)and nitrous oxide(greenhouse gas).Enrichment of animal,plant,and human pathogens means that the plastisphere could become an increasingly mobile reservoir of harmful microorganisms.Our findings highlight that if the trajectory of plastic emissions is not reversed,the expanding plastisphere could pose critical planetary health challenges.

关键词： reservoir mostly habitat

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environmental benefits and farmers' adoption of winter cover crops in the North China Plain

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Pedosphere 2024年第1期34卷 159-169页

作者： Shufang GUO Yitao ZHANG Limei ZHAI Jian LIU Hongyuan WANG Hongbin LIU state key laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China Key Laboratory of Nonpoint Source Pollution ControlMinistry of Agriculture and Rural AffairsInstitute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijing 100081China institute of Agricultural Environment and resources Yunnan Academy of Agricultural SciencesKunming 650205China Shandong Yucheng Agro-ecosystem National Observation research Station Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of SciencesBeijing 100101China The Norwegian institute of Bioeconomy research(NIBIO) Akershus 1431Norway

The introduction of cover crops into monoculture systems to improve soil health has been widely adopted worldwide. However, little is known about the environmental risks and application prospects of different cover crops in spring maize(Zea mays L.) monocultures proposed in the North China Plain. A pot experiment was conducted to evaluate the effects of different winter cover crops on subsequent maize yield, soil fertility, and environmental risks of nitrogen(N) loss, and a questionnaire survey was conducted to examine factors influencing farmers' willingness to adopt cover crops in the North China Plain. Based on the same fertilization regime during the maize growing period, four winter cover crop treatments were set up, including bare fallow, hairy vetch(Vicia villosa Roth.), February orchid(Orychophragmus violaceus), and winter oilseed rape(Brassica campestris L.). The results indicated that winter cover crops significantly increased subsequent maize yield and soil organic carbon, total N, and microbial biomass carbon and N compared with the bare fallow treatment.The incorporation of cover crops led to a negligible increase in nitrous oxide(N_(2)O) emissions and had a very limited effect on ammonia(NH_(3)) emissions.The incorporation of February orchid and winter oilseed rape decreased nitrate leaching compared with the hairy vetch treatment in the maize growing season.The N losses via N_(2)O and NH_(3) emissions and N leaching accounted for 71%–84% of the N surplus. However, yield increase and environmental benefits were not the main positive factors for farmers to accept cover crops. Financial incentive was rated by 83.9% of farmers as an “extremely important” factor, followed by other costs, when considering winter cover cropping. These results indicate that the environmental benefits depend on the type of cover crop. Maintaining high levels of soil fertility and maize yield, providing sufficient subsidies, and encouraging large-area cultivation of cover crops are critical measures to promote winter cover c

关键词： cover crop N leaching NH_(3)emission N_(2)O emission spring maize willingness to accept

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Enhanced organic degradation and microbial community cooperation by inoculating Bacillus licheniformis in low temperature composting

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Journal of environmental Sciences 2024年第9期143卷 189-200页

作者： Jing Su Kaiyun Zhou Wenjie Chen Shaoqi Xu Ziwei Feng Yuan Chang Xiaoyan Ding Yi Zheng Xingling Tao Ake Zhang Yue Wang Ji Li Guochun Ding Yuquan Wei Nanjing institute of environmental Sciences Ministry of Ecology and EnvironmentNanjing 210042China College of resources and environmental Science Beijing Key Laboratory of Biodiversity and Organic FarmingChina Agricultural UniversityBeijing 100193China Organic Recycling institute(Suzhou)of China Agricultural University Wuzhong DistrictSuzhou 215128China Fuyang Academy of Agricultural Sciences Fuyang 236065China

microbial activity and interaction are the important driving factors in the start-up phase of food waste composting at low temperature.The aim of this study was to explore the effect of inoculating Bacillus licheniformis on the degradation of organic components and the potential microbe-driven mechanism from the aspects of organic matter degradation,enzyme activity,microbial community interaction,and microbial metabolic function.The results showed that after inoculating B.licheniformis,temperature increased to 47.8℃ on day2,and the degradation of readily degraded carbohydrates(RDC)increased by 31.2%,and the bioheat production increased by 16.5%.There was an obvious enhancement of extracellular enzymes activities after inoculation,especially amylase activity,which increased by 7.68 times on day 4.The inoculated B.licheniformis colonized in composting as key genus in the start-up phase.Modular network analysis and Mantel test indicated that inoculation drove the cooperation between microbial network modules who were responsible for various organic components(RDC,lipid,protein,and lignocellulose)degradation in the start-up phase.Metabolic function prediction suggested that carbohydrate metabolisms including starch and sucrose metabolism,glycolysis/gluconeogenesis,pyruvate metabolism,etc.,were improved by increasing the abundance of related functional genes after inoculation.In conclusion,inoculating B.licheniformis accelerated organic degradation by driving the cooperation between microbial network modules and enhancing microbial metabolism in the start-up phase of composting.

关键词： microbial agent Organic matter degradation microbial interaction Food waste Low temperature composting

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